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Binding site mapping of protein ligands
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JBP PDB entry 2JBP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 273 40% ethanol, 5% PEG1000, 100mM phosphate-citrate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 273K
Crystal Properties Matthews coefficient Solvent content 3.04 59.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.208 α = 90 b = 183.192 β = 90 c = 217.656 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2008-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9720 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 3.2 46.73 99.3 0.173 0.173 4.02 129778 91154 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.31 100 0.63 0.012 1.2 3.99
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2JBP 3.2 46.73 92915 88052 4642 99.76 0.23909 0.23807 0.25817 0.2591 RANDOM 65.458
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.24 0.46 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.87 r_dihedral_angle_4_deg 19.828 r_dihedral_angle_3_deg 19.718 r_dihedral_angle_1_deg 5.502 r_scangle_it 2.725 r_angle_refined_deg 1.608 r_scbond_it 1.499 r_mcangle_it 1.43 r_mcbond_it 0.741 r_chiral_restr 0.091
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.87 r_dihedral_angle_4_deg 19.828 r_dihedral_angle_3_deg 19.718 r_dihedral_angle_1_deg 5.502 r_scangle_it 2.725 r_angle_refined_deg 1.608 r_scbond_it 1.499 r_mcangle_it 1.43 r_mcbond_it 0.741 r_chiral_restr 0.091 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 27956 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 312
Software Software Software Name Purpose DNA data collection PHASER phasing REFMAC refinement CrystalClear data reduction CrystalClear data scaling